Manyuan Long, Ph.D. Professor Department of Ecology & Evolution Biological Sciences Collegiate Division Office: Zoology 301E | Phone: (773) 702-0557 | Fax: (773) 702-9740 | email:mlong(at)uchicago(dot)edu Subjects: Molecular evolution, evolutionary genomics Long Lab Home Page

Research Interests

An interesting problem in evolutionary biology is how genes with novel functions originate. My research focuses on this problem, although I am also interested in other issues of molecular evolution. Interest in evolutionary novelties can be traced back to the time of Darwin. However, studies of the origin and evolution of genes with new functions have only recently become possible and attracted increasing attention. Although conceptual revolution is always what we wish to pursue, the available molecular techniques and rapidly expanded genome data from many organisms mean that searching for and characterizing new genes is no longer a formidable technical obstacle. Molecular and evolutionary studies have provided powerful analytical tools for the detection of the processes and mechanisms that underlie the origin of new genes.

Three levels of questions about this process can be defined. First, at the level of individual new genes, what are the initial molecular mechanisms that generate new gene structures? Once a new gene arises in an individual genome in a natural population, how does it spread throughout an entire species to become fixed? And, how does the young gene subsequently evolve? Second, at the level of the genome, how often do new genes originate? If new gene formation is not a rare event, are there any patterns that underlie the process? And, what evolutionary and genetic mechanisms govern any such patterns? Third, what are functions and phenotypic effects of new genes? How are the detected patterns impacting the phenotypic evolution, e.g. the environmental adaptation and the courtship behavior evolution?

I believe that an efficient approach to these questions is to examine young genes because their early processes of origination are directly observable. Pursuit of these problems requires an integrated approach incorporating molecular, genomic and population analyses. My lab applies such an approach to our studies. Using experimental and computational genomic analysis, we identified numerous new genes in Drosophila and mammalian genomes. Using molecular analysis, we revealed some important molecular evolutionary mechanisms responsible for their current gene structures. By evolutionary genetic analysis, we observed a significant role of the adaptive evolution in the determination of the fate of those new genes. Interesting patterns are observed associated with these new genes.

I see questions there, challenges there, joys there...

Selected Publications

Vibranovski MD, Zhang Y, Long M, 2009. General gene movement off the X chromosome in the Drosophila genus. Genome Research 19: 897-903.

Kaessmann H, Vinckenbosch N, and Long M, 2009. RNA-based gene duplication. Nature Reviews Genetics 10: 19-31.

Yang S., Arguello R, Li X, Ding Y, Zhou Q, Chen Y, Zhang Y, Zhao R, Brunet F, Peng L, Long M, Wang W., 2008. Repetitive Elements-mediated Recombination as a Mechanism for New Gene Origination in Drosophila PLoS Genetics 4(1): e3. 0001-0010.

Dai H, Chen Y, Chen S, Mao Q, Kennedy D, Landback P, Eyre-Walker A, Du D, Long M, 2008. The evolution of courtship behaviors through the origination of a new gene in Drosophila. Proc Natl Acad Sci USA. 105:7478-83.

Emerson JJ, Cardoso-Moreira M, Borevitz JO, Long M, 2008. Natural selection shapes genome wide patterns of copy number polymorphism in D. melanogaster. Science 320:1629-1631.

Long M., 2007. Journal Club: Mystery Genes. Nature 449: 511.

Drosophila 12 Genomes Consortium, 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218.

Arguello JR, Chen Y, Yang S, Wang W, and Long M, 2006. An X-linked Testes Chimeric Gene by Illegitimate Recombination in Drosophila. PLoS Genetics 2: 0745-0754. e77.

Wang W, Zheng H, Fan C, Li J, Shi J, Cai Z, et al, 2006. High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell 18: 1791-1802.

Zhang, J., A. M. Dean, F. Brunet and M. Long 2004. Evolving functional diversity in new genes of Drosophila. Proc Natl Acad Sci USA. 101: 16246-16250.

Wang, W., H. Yu and M. Long 2004. Duplication-degeneration as a mechanism of gene fission and the origin of Drosophila new genes. Nature Genetics 36: 523 527.

Emerson J.J., H. Kaesmann, E. Betrán and M. Long 2004. Extensive gene traffic on the human X chromosome. Science 303: 537-540.

International Chicken Genome Sequencing Consortium. 2004, Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716.

Long, M., E. Betrán, K. Thornton, and W. Wang. 2003. The origin of new genes: glimpses from the young and old. Nature Reviews Genetics 4: 865-875.

Llopart, A., J. M. Comeron, F. G. Brunet, D. Lachaise, M. Long 2002. Intron presence / absence polymorphism in Drosophila driven by positive Darwinian selection. Proc. Natl. Acad. Sci. USA

Betrán, E., K. Thornton, and M. Long 2002. Retroposed new genes out of the X in Drosophila. Genome Res. 12: 1854-1859.

Wang, W., K. Thornton, A. Berry, and M. Long. 2002. Nucleotide variation along the Drosophila melanogaster fourth chromosome. Science 295:134-137.

Wang, W., F. G. Brunet, E. Nevo, M. Long 2002. Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA.. 99: 4448-4453.

Long, M. 2001. Evolution of novel genes. Curr. Opin. Genet. Dev. 11:673-680.

Long, M., K. Thornton 2001. Gene duplication and evolution. Science 293:1551.

Cáceres, M., J. M. Ranz, Barbadilla, M. Long, and A. Ruiz 1999, Generation of a widespread Drosophila inversion by a transposable element. Science 285: 415-418.

De Souza, S. J., M. Long, R. J. Klein, S. Roy, S. Lin, W. Gilbert 1998. Towards a resolution of the introns early/late debate. Only phase zero introns are correlated with the structure of ancient proteins. Proc. Natl. Acad. Sci. USA 95: 5094-5099.

Long, M., S.J. de Souza, W. Gilbert 1998. Relationship between "proto-splice sites" and intron phases: Evidence from Dicodon Analysis. Proc. Natl. Acad. Sci. USA 95: 219-223.

Long, M., S.J. De Souza, W. Gilbert 1997. The yeast splice site revisited: A new exon consensus from genomic analysis. Cell 91: 739-740.

Gilbert, W., S.J. De Souza, M. Long 1997. Origin of genes. Proc. Natl. Acad. Sci. USA 94: 7698-7703.

Long, M., S.J. De Souza, W. Gilbert 1997. Delta-interacting protein A and the origin of hepatitis delta antigen. Science 276: 824-825.

Long, M., S. J. De Souza, C. Rosenberg, W. Gilbert 1996. Exon shuffling and origin of plant mitochondrial targeting targeting in cytochrome c1 precursor. Proc. Natl. Acad. Sci. USA 93: 7727-7731.

De Souza, S. J., M. Long, L. Schoenbach, W. Gilbert 1996. Intron positions correlate with module boundaries in ancient proteins. Proc. Natl. Acad. Sci. USA 93: 14632-14636.

Long, M., C. Rosenberg, W. Gilbert 1995. Intron phase correlations and the evolution of intron/exon structure of genes. Proc. Natl. Acad. Sci. USA 92: 12495-12499.

Long, M, S. J. de Souza, W. Gilbert 1995. Evolution of intron/exon structure of eukaryotic genes. Curr. Opin. Genet. Dev. 5: 774-778.

Long, M., C. H. Langley 1993. Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science 260: 91-95.

Long, M. ed. 2003 Origin and Evolution of New Gene Functions. (Volume 10, Contemporary Issues in Genetics and Evolution and Volume 118 (2-3), Genetica). Kluwer Academic Publishers, The Netherlands. 202 pages.